A new approach to enhancing proton conductivity of ceramic is demonstrated by aligning proton conductive pathways and eliminating resistive grain boundaries. Hydroxyapatite (HAP) membranes are synthesized by multistage crystallization onto palladium. The synthesis involves three steps: electrochemical deposition of HAP seeds, secondary hydrothermal crystallization onto the seed layer to promote c-axis growth normal to the substrate, and tertiary hydrothermal crystallization to promote a-axis growth to fill the gaps between the aligned crystals. The c-axis alignment with crystal domains spanning the membrane thickness significantly enhances proton conduction since protons are primarily transported along the c-axes of HAP crystals. The novel HAP membranes display proton conductivity almost four orders of magnitude higher than traditional sintered HAP ceramics. The HAP membranes on palladium hydrogen membrane substrates hold promise for use in intermediate-temperature fuel cells, chemical sensors, and other devices. The synthesis approach presented may also be applied to other ion-conducting membrane materials to enhance transport properties.